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export from tome to any other format? #29
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Hi Max, .tome files are an HDF5-formatted sparse matrix format, so you should be able to extract the data back out to .h5 (following 10x conventions) or .mtx. Here are some examples in R (below). If your target is Python, let me know. I think I have some code that may be able to go straight from .tome into a scipy sparse csc matrix. For .mtx
There is a 10x .h5 output function (
I wouldn't recommend a .csv or .tsv, as expanding these files out to full matrices instead of sparse formats can make the resulting files very large. However, there is a .csv export function,
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Hi, would it be possible to provide these files in some other format, like .mtx? Getting all these packages to work on our server is painful, it requires a certain version of R and just for reading a few files, this seems a lot of work. Would you mind providing these files in some other format, besides your own file format? It would be very much appreciated and may help increase community uptake of your results... |
Hello, I got the following error when I used it. Could you tell me the reason?sample_name <- read_tome_sample_names(tome)
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Hello wuzhaoqi1015, From both of your inquiries, it seems like you might be missing to load the test dataset properly. Try this: library(scrattch.io) tome <- system.file("testdata/tome", |
Thank you for your reply to the previous message. I have some questions to ask. [1] "Writing rows 1 to 2000" Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 0, 2000` |
Hi wuzhaoqi1015, be assured that everyone has the same problem as you.
I think the authors should provide all expression matrices in a normal
format that anyone can read, ideally as text-based csv files, one for the
matrix, one for the meta data.
…On Fri, Apr 3, 2020 at 10:35 AM wuzhaoqi1015 ***@***.***> wrote:
Thank you for your reply to the previous message. I have some questions to
ask.
1.I wanna get a matrix with row and column names. After extracting the
sparse matrix, can I add column and row names as follows?
a<-read_tome_dgCMatrix(tome,"data/t_exon") # read exon
b<-read_tome_dgCMatrix(tome,"data/t_intron") #read intron sample_name <-
read_tome_sample_names(tome) gene_name <- read_tome_gene_names(tome)
rownames(a)<-gene_name colnames(a)<-sample_name
2.I want to export this matrix to a file. But when I run
“write_dgCMatrix_csv”, I get an error. What is the reason for it? Is it
possible to use "as.matrix" and then "write.csv".
[image: image]
<https://user-images.githubusercontent.com/52707572/78340662-10442880-75c9-11ea-988f-4cd4987f7044.png>
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I am also getting this error:
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Hi, we have a tome file that we need to process. Is there any function or way to get the data out of the .tome file in a standard format? Like .mtx, .h5, a .csv or .tsv file with the genes on the lines and the first column being the geneId (possibly the symbol separated by | or similar) ?
I can see that tome is very good at importing files, but I cannot see an export function...
thanks!
Max
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